What about the pertussis vaccine and the fact that we are finding more and more strains of pertactin-negative pertussis bacteria? Doesn’t that mean that the Bordetella pertussis bacteria have mutated and are causing a pertussis resurgence because they are resistant to the vaccine?

While an interesting theory, pertactin is only one of the components (antigens) of the pertussis bacteria that are in pertussis vaccines that help them to induce immunity. Others can include filamentous hemagglutinin, chemically or genetically detoxified pertussis toxin, and fimbrial-2 and fimbrial-3 antigens.

So no, pertactin-negative pertussis bacteria are not driving outbreaks of pertussis or whooping cough, and they have not become resistant to pertussis vaccines.

Vaccine-Induced Pathogen Strain Replacement

What about the fact that we sometimes seen a rise in new bacteria once a vaccine wipes out the bacteria it works against?

While this type of vaccine-induced pathogen strain or serotype replacement can happen, it is not because the bacteria develop any kind of resistance. Some vaccines can only target specific strains of a virus or bacteria. The latest version of Prevnar, for example, can prevent the 13 strains of Streptococcal pneumonia that are most likely to cause disease in children. That leaves out over 75 other strains.

And the Hib vaccine only prevents Haemophilus influenzae type b infections. There are five other H. flu serotypes (a-f) and other non-typeable strains that aren’t covered by the Hib vaccine.